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source: trunk/GSASIIIO.py @ 4573

Last change on this file since 4573 was 4573, checked in by toby, 2 years ago
RB extensions and minor bug fixes
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2020-09-21 20:43:06 +0000 (Mon, 21 Sep 2020) $
4	# $Author: toby $
5	# $Revision: 4573 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 4573 2020-09-21 20:43:06Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base class for data export routines (TODO: should move)
19
20	TODO: This module needs some work to separate wx from non-wx routines. GUI
21	routines should probably move to GSASIIctrlGUI.
22	'''
23
24	from __future__ import division, print_function
25
26	# Allow this to be imported without wx present. Was needed for G2scriptable, but is
27	# likely not needed anymore
28	try:
29	import wx
30	except ImportError:
31	# was needed by sphinx, but probably not anymore
32	class Placeholder(object):
33	def __init__(self):
34	self.Dialog = object
35	wx = Placeholder()
36	import math
37	import numpy as np
38	import numpy.ma as ma
39
40	import copy
41	import platform
42	if '2' in platform.python_version_tuple()[0]:
43	import cPickle
44	else:
45	import pickle as cPickle
46	import sys
47	import re
48	import random as ran
49	import GSASIIpath
50	GSASIIpath.SetVersionNumber("$Revision: 4573 $")
51	try:
52	import GSASIIdataGUI as G2gd
53	except ImportError:
54	pass
55	import GSASIIobj as G2obj
56	import GSASIIlattice as G2lat
57	try:
58	import GSASIIpwdGUI as G2pdG
59	import GSASIIimgGUI as G2imG
60	except ImportError:
61	pass
62	import GSASIIElem as G2el
63	import GSASIIstrIO as G2stIO
64	import GSASIImapvars as G2mv
65	import GSASIIfiles as G2fil
66	try:
67	import GSASIIctrlGUI as G2G
68	except ImportError:
69	pass
70	import os
71	import os.path as ospath
72
73	DEBUG = False #=True for various prints
74	TRANSP = False #=true to transpose images for testing
75	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
76	npsind = lambda x: np.sin(x*np.pi/180.)
77
78	def sfloat(S):
79	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
80	if S.strip():
81	try:
82	return float(S)
83	except ValueError:
84	pass
85	return 0.0
86
87	def sint(S):
88	'Convert a string to int. An empty field is treated as zero'
89	if S.strip():
90	return int(S)
91	else:
92	return 0
93
94	def trim(val):
95	'''Simplify a string containing leading and trailing spaces
96	as well as newlines, tabs, repeated spaces etc. into a shorter and
97	more simple string, by replacing all ranges of whitespace
98	characters with a single space.
99
100	:param str val: the string to be simplified
101
102	:returns: the (usually) shortened version of the string
103	'''
104	return re.sub('\s+', ' ', val).strip()
105
106	def FileDlgFixExt(dlg,file):
107	'this is needed to fix a problem in linux wx.FileDialog'
108	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
109	if ext not in file:
110	file += ext
111	return file
112
113	def GetPowderPeaks(fileName):
114	'Read powder peaks from a file'
115	sind = lambda x: math.sin(x*math.pi/180.)
116	asind = lambda x: 180.*math.asin(x)/math.pi
117	wave = 1.54052
118	File = open(fileName,'Ur')
119	Comments = []
120	peaks = []
121	S = File.readline()
122	while S:
123	if S[:1] == '#':
124	Comments.append(S[:-1])
125	else:
126	item = S.split()
127	if len(item) == 1:
128	peaks.append([float(item[0]),1.0])
129	elif len(item) > 1:
130	peaks.append([float(item[0]),float(item[0])])
131	S = File.readline()
132	File.close()
133	if Comments:
134	print ('Comments on file:')
135	for Comment in Comments:
136	print (Comment)
137	if 'wavelength' in Comment:
138	wave = float(Comment.split('=')[1])
139	Peaks = []
140	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
141	for peak in peaks:
142	dsp = peak[0]
143	sth = wave/(2.0*dsp)
144	if sth < 1.0:
145	tth = 2.0*asind(sth)
146	else:
147	break
148	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
149	else: #2-thetas - assume Cuka (for now)
150	for peak in peaks:
151	tth = peak[0]
152	dsp = wave/(2.0*sind(tth/2.0))
153	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
154	limits = [1000.,0.]
155	for peak in Peaks:
156	limits[0] = min(limits[0],peak[0])
157	limits[1] = max(limits[1],peak[0])
158	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
159	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
160	return Comments,Peaks,limits,wave
161
162	def GetCheckImageFile(G2frame,treeId):
163	'''Try to locate an image file if the project and image have been moved
164	together. If the image file cannot be found, request the location from
165	the user.
166
167	:param wx.Frame G2frame: main GSAS-II Frame and data object
168	:param wx.Id treeId: Id for the main tree item for the image
169	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
170	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
171	and (imagetag) an optional image number
172
173	'''
174	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
175	if isinstance(Imagefile,list):
176	imagefile,imagetag = Imagefile
177	else:
178	imagefile = Imagefile
179	if not os.path.exists(imagefile):
180	print ('Image file '+imagefile+' not found')
181	fil = imagefile.replace('\\','/') # windows?!
182	# see if we can find a file with same name or in a similarly named sub-dir
183	pth,fil = os.path.split(fil)
184	prevpth = None
185	while pth and pth != prevpth:
186	prevpth = pth
187	if os.path.exists(os.path.join(G2frame.dirname,fil)):
188	print ('found image file '+os.path.join(G2frame.dirname,fil))
189	imagefile = os.path.join(G2frame.dirname,fil)
190	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
191	return Npix,imagefile,imagetag
192	pth,enddir = os.path.split(pth)
193	fil = os.path.join(enddir,fil)
194	# not found as a subdirectory, drop common parts of path for last saved & image file names
195	# if image was .../A/B/C/imgs/ima.ge
196	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
197	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
198	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
199	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
200	imgPath = imagefile.replace('\\','/').split('/')
201	for p1,p2 in zip(gpxPath,imgPath):
202	if p1 == p2:
203	gpxPath.pop(0),imgPath.pop(0)
204	else:
205	break
206	fil = os.path.join(*imgPath) # file with non-common prefix elements
207	prevpth = None
208	pth = os.path.abspath(G2frame.dirname)
209	while pth and pth != prevpth:
210	prevpth = pth
211	if os.path.exists(os.path.join(pth,fil)):
212	print ('found image file '+os.path.join(pth,fil))
213	imagefile = os.path.join(pth,fil)
214	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
215	return Npix,imagefile,imagetag
216	pth,enddir = os.path.split(pth)
217	#GSASIIpath.IPyBreak()
218
219	if not os.path.exists(imagefile):
220	# note that this fails (at least on Mac) to get an image during the GUI initialization
221	prevnam = os.path.split(imagefile)[1]
222	prevext = os.path.splitext(imagefile)[1]
223	wildcard = 'Image format ('+prevext+')\|'+prevext
224	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
225	wildcard,wx.FD_OPEN)
226	try:
227	dlg.SetFilename(''+ospath.split(imagefile)[1])
228	if dlg.ShowModal() == wx.ID_OK:
229	imagefile = dlg.GetPath()
230	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
231	else:
232	imagefile = None # was False
233	finally:
234	dlg.Destroy()
235	return Npix,imagefile,imagetag
236
237	def EditImageParms(parent,Data,Comments,Image,filename):
238	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
239	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
240	def onClose(event):
241	dlg.EndModal(wx.ID_OK)
242	mainsizer = wx.BoxSizer(wx.VERTICAL)
243	h,w = Image.shape[:2]
244	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
245	0,wx.ALIGN_LEFT\|wx.ALL, 2)
246
247	vsizer = wx.BoxSizer(wx.HORIZONTAL)
248	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
249	0,wx.ALIGN_LEFT\|wx.ALL, 2)
250	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
251	vsizer.Add(wdgt)
252	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
253
254	vsizer = wx.BoxSizer(wx.HORIZONTAL)
255	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
256	0,wx.ALIGN_LEFT\|wx.ALL, 2)
257	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,size=(50,-1))
258	vsizer.Add(wdgt)
259	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
260	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
261	vsizer.Add(wdgt)
262	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
263
264	vsizer = wx.BoxSizer(wx.HORIZONTAL)
265	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
266	0,wx.ALIGN_LEFT\|wx.ALL, 2)
267	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
268	vsizer.Add(wdgt)
269	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
270
271	vsizer = wx.BoxSizer(wx.HORIZONTAL)
272	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
273	0,wx.ALIGN_LEFT\|wx.ALL, 2)
274	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
275	vsizer.Add(wdgt)
276	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
277	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
278	vsizer.Add(wdgt)
279	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
280
281	vsizer = wx.BoxSizer(wx.HORIZONTAL)
282	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
283	0,wx.ALIGN_LEFT\|wx.ALL, 2)
284	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
285	vsizer.Add(wdgt)
286	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
287
288	btnsizer = wx.StdDialogButtonSizer()
289	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
290	OKbtn.SetDefault()
291	OKbtn.Bind(wx.EVT_BUTTON,onClose)
292	btnsizer.AddButton(OKbtn) # not sure why this is needed
293	btnsizer.Realize()
294	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
295	dlg.SetSizer(mainsizer)
296	dlg.CenterOnParent()
297	dlg.ShowModal()
298
299	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
300	'''Load an image into the tree. Saves the location of the image, as well as the
301	ImageTag (where there is more than one image in the file), if defined.
302	'''
303	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
304	TreeLbl = 'IMG '+os.path.basename(imagefile)
305	ImageTag = Data.get('ImageTag')
306	if ImageTag:
307	TreeLbl += ' #'+'%04d'%(ImageTag)
308	imageInfo = (imagefile,ImageTag)
309	else:
310	imageInfo = imagefile
311	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
312	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
313	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
314	Imax = np.amax(Image)
315	if G2frame.imageDefault:
316	Data = copy.copy(G2frame.imageDefault)
317	Data['showLines'] = True
318	Data['ring'] = []
319	Data['rings'] = []
320	Data['cutoff'] = 10.
321	Data['pixLimit'] = 20
322	Data['edgemin'] = 100000000
323	Data['calibdmin'] = 0.5
324	Data['calibskip'] = 0
325	Data['ellipses'] = []
326	Data['calibrant'] = ''
327	Data['GonioAngles'] = [0.,0.,0.]
328	Data['DetDepthRef'] = False
329	else:
330	Data['type'] = 'PWDR'
331	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
332	if 'tilt' not in Data: #defaults if not preset in e.g. Bruker importer
333	Data['tilt'] = 0.0
334	Data['rotation'] = 0.0
335	Data['pixLimit'] = 20
336	Data['calibdmin'] = 0.5
337	Data['cutoff'] = 10.
338	Data['showLines'] = False
339	Data['calibskip'] = 0
340	Data['ring'] = []
341	Data['rings'] = []
342	Data['edgemin'] = 100000000
343	Data['ellipses'] = []
344	Data['GonioAngles'] = [0.,0.,0.]
345	Data['DetDepth'] = 0.
346	Data['DetDepthRef'] = False
347	Data['calibrant'] = ''
348	Data['IOtth'] = [5.0,50.0]
349	if GSASIIpath.GetConfigValue('Image_2theta_min'):
350	try:
351	Data['IOtth'][0] = float(GSASIIpath.GetConfigValue('Image_2theta_min'))
352	except:
353	pass
354	if GSASIIpath.GetConfigValue('Image_2theta_max'):
355	try:
356	Data['IOtth'][1] = float(GSASIIpath.GetConfigValue('Image_2theta_max'))
357	except:
358	pass
359	Data['LRazimuth'] = [0.,180.]
360	Data['azmthOff'] = 0.0
361	Data['outChannels'] = 2500
362	Data['outAzimuths'] = 1
363	Data['centerAzm'] = False
364	Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True)
365	Data['setRings'] = False
366	Data['background image'] = ['',-1.0]
367	Data['dark image'] = ['',-1.0]
368	Data['Flat Bkg'] = 0.0
369	Data['Oblique'] = [0.5,False]
370	Data['setDefault'] = False
371	Data['range'] = [(0,Imax),[0,Imax]]
372	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
373	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],
374	'Thresholds':[(0,Imax),[0,Imax]],
375	'SpotMask':{'esdMul':3.,'spotMask':None}}
376	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
377	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
378	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
379	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
380	G2frame.PickId = Id
381	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
382	G2frame.Image = Id
383
384	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
385	'''Read a single image with an image importer. This is called to reread an image
386	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
387	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
388
389	:param wx.Frame G2frame: main GSAS-II Frame and data object.
390	:param str imagefile: name of image file
391	:param bool imageOnly: If True return only the image,
392	otherwise (default) return more (see below)
393	:param int/str ImageTag: specifies a particular image to be read from a file.
394	First image is read if None (default).
395	:param str formatName: the image reader formatName
396
397	:returns: an image as a numpy array or a list of four items:
398	Comments, Data, Npix and the Image, as selected by imageOnly
399
400	'''
401	# determine which formats are compatible with this file
402	primaryReaders = []
403	secondaryReaders = []
404	for rd in G2frame.ImportImageReaderlist:
405	flag = rd.ExtensionValidator(imagefile)
406	if flag is None:
407	secondaryReaders.append(rd)
408	elif flag:
409	if not FormatName:
410	primaryReaders.append(rd)
411	elif FormatName == rd.formatName:
412	primaryReaders.append(rd)
413	if len(secondaryReaders) + len(primaryReaders) == 0:
414	print('Error: No matching format for file '+imagefile)
415	raise Exception('No image read')
416	errorReport = ''
417	if not imagefile:
418	return
419	for rd in primaryReaders+secondaryReaders:
420	rd.ReInitialize() # purge anything from a previous read
421	rd.errors = "" # clear out any old errors
422	if not rd.ContentsValidator(imagefile): # rejected on cursory check
423	errorReport += "\n "+rd.formatName + ' validator error'
424	if rd.errors:
425	errorReport += ': '+rd.errors
426	continue
427	if imageOnly:
428	ParentFrame = None # prevent GUI access on reread
429	else:
430	ParentFrame = G2frame
431	if GSASIIpath.GetConfigValue('debug'):
432	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
433	else:
434	flag = False
435	try:
436	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
437	except rd.ImportException as detail:
438	rd.errors += "\n Read exception: "+str(detail)
439	except Exception as detail:
440	import traceback
441	rd.errors += "\n Unhandled read exception: "+str(detail)
442	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
443	if flag: # this read succeeded
444	if rd.Image is None:
445	raise Exception('No image read. Strange!')
446	if GSASIIpath.GetConfigValue('Transpose'):
447	print ('Transposing Image!')
448	rd.Image = rd.Image.T
449	#rd.readfilename = imagefile
450	if imageOnly:
451	return rd.Image
452	else:
453	return rd.Comments,rd.Data,rd.Npix,rd.Image
454	else:
455	print('Error reading file '+imagefile)
456	print('Error messages(s)\n'+errorReport)
457	raise Exception('No image read')
458
459	def ReadImages(G2frame,imagefile):
460	'''Read one or more images from a file and put them into the Tree
461	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
462
463	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
464	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
465	it would be good if these routines used a common code core so that changes need to
466	be made in only one place.
467
468	:param wx.Frame G2frame: main GSAS-II Frame and data object.
469	:param str imagefile: name of image file
470
471	:returns: a list of the id's of the IMG tree items created
472	'''
473	# determine which formats are compatible with this file
474	primaryReaders = []
475	secondaryReaders = []
476	for rd in G2frame.ImportImageReaderlist:
477	flag = rd.ExtensionValidator(imagefile)
478	if flag is None:
479	secondaryReaders.append(rd)
480	elif flag:
481	primaryReaders.append(rd)
482	if len(secondaryReaders) + len(primaryReaders) == 0:
483	print('Error: No matching format for file '+imagefile)
484	raise Exception('No image read')
485	errorReport = ''
486	rdbuffer = {} # create temporary storage for file reader
487	for rd in primaryReaders+secondaryReaders:
488	rd.ReInitialize() # purge anything from a previous read
489	rd.errors = "" # clear out any old errors
490	if not rd.ContentsValidator(imagefile): # rejected on cursory check
491	errorReport += "\n "+rd.formatName + ' validator error'
492	if rd.errors:
493	errorReport += ': '+rd.errors
494	continue
495	ParentFrame = G2frame
496	block = 0
497	repeat = True
498	CreatedIMGitems = []
499	while repeat: # loop if the reader asks for another pass on the file
500	block += 1
501	repeat = False
502	if GSASIIpath.GetConfigValue('debug'):
503	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
504	else:
505	flag = False
506	try:
507	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
508	except rd.ImportException as detail:
509	rd.errors += "\n Read exception: "+str(detail)
510	except Exception as detail:
511	import traceback
512	rd.errors += "\n Unhandled read exception: "+str(detail)
513	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
514	if flag: # this read succeeded
515	if rd.Image is None:
516	raise Exception('No image read. Strange!')
517	if GSASIIpath.GetConfigValue('Transpose'):
518	print ('Transposing Image!')
519	rd.Image = rd.Image.T
520	rd.Data['ImageTag'] = rd.repeatcount
521	rd.readfilename = imagefile
522	# Load generic metadata, as configured
523	G2fil.GetColumnMetadata(rd)
524	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
525	repeat = rd.repeat
526	CreatedIMGitems.append(G2frame.Image)
527	if CreatedIMGitems: return CreatedIMGitems
528	else:
529	print('Error reading file '+imagefile)
530	print('Error messages(s)\n'+errorReport)
531	return []
532	#raise Exception('No image read')
533
534	def SaveMultipleImg(G2frame):
535	if not G2frame.GPXtree.GetCount():
536	print ('no images!')
537	return
538	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
539	if len(choices) == 1:
540	names = choices
541	else:
542	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
543	dlg.SetSelections([])
544	names = []
545	if dlg.ShowModal() == wx.ID_OK:
546	names = [choices[sel] for sel in dlg.GetSelections()]
547	dlg.Destroy()
548	if not names: return
549	for name in names:
550	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
551	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
552	imroot = os.path.splitext(imagefile)[0]
553	if imagetag:
554	imroot += '_' + str(imagetag)
555	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
556	print('Writing '+imroot+'.imctrl')
557	File = open(imroot+'.imctrl','w')
558	keys = ['type','wavelength','calibrant','distance','center',
559	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
560	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
561	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
562	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
563	for key in keys:
564	if key not in Data: continue #uncalibrated!
565	File.write(key+':'+str(Data[key])+'\n')
566	File.close()
567	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
568	G2imG.CleanupMasks(mask)
569	print('Writing '+imroot+'.immask')
570	File = open(imroot+'.immask','w')
571	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
572	File.write(key+':'+str(mask[key])+'\n')
573	File.close()
574
575	def PutG2Image(filename,Comments,Data,Npix,image):
576	'Write an image as a python pickle - might be better as an .edf file?'
577	File = open(filename,'wb')
578	cPickle.dump([Comments,Data,Npix,image],File,2)
579	File.close()
580	return
581
582	objectScanIgnore = [int,bool,float,str,np.float64,np.float32,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,G2obj.ExpressionObj]
583	try:
584	objectScanIgnore += [ma.MaskedArray] # fails in doc builds
585	except AttributeError:
586	pass
587
588	if '2' in platform.python_version_tuple()[0]:
589	objectScanIgnore += [unicode,long,]
590
591	def objectScan(data,tag,indexStack=[]):
592	'''Recursively scan an object looking for unexpected data types.
593	This is used in debug mode to scan .gpx files for objects we did not
594	intend to be there.
595	'''
596	if type(data) is list or type(data) is tuple:
597	for i in range(len(data)):
598	val = objectScan(data[i],tag,indexStack+[i])
599	if val:
600	data[i] = val
601	print('...fixed')
602	elif type(data) is dict:
603	for key in data:
604	val = objectScan(data[key],tag,indexStack+[key])
605	if val:
606	data[key] = val
607	print('...fixed')
608	elif data is None:
609	return None
610	elif type(data) in objectScanIgnore:
611	return None
612	else:
613	s = 'unexpected object in '+tag
614	for i in indexStack:
615	s += "[{}]".format(i)
616	#print(s,data.__class__.__name__) # loses full name of class
617	print(s,type(data))
618	global unexpectedObject
619	unexpectedObject = True
620	# fix bad objects
621	if "gdi.Colour" in str(type(data)):
622	return tuple(data)
623	return
624
625	def cPickleLoad(fp):
626	if '2' in platform.python_version_tuple()[0]:
627	return cPickle.load(fp)
628	else:
629	return cPickle.load(fp,encoding='latin-1')
630
631	def ProjFileOpen(G2frame,showProvenance=True):
632	'Read a GSAS-II project file and load into the G2 data tree'
633	if not os.path.exists(G2frame.GSASprojectfile):
634	print ('\n*** Error attempt to open project file that does not exist:\n '+
635	str(G2frame.GSASprojectfile))
636	return
637	LastSavedUsing = None
638	filep = open(G2frame.GSASprojectfile,'rb')
639	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
640	GPXphase = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqPhase'
641	GPXhist = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqHist'
642	deleteSeq = False
643	hist = None
644	tmpHistIndex = {}
645	updateFromSeq = False
646	if os.path.exists(GPXphase) and os.path.exists(GPXhist):
647	dlg = wx.MessageDialog(G2frame,
648	'Load results from crashed sequential fit?\nNo deletes the files!', 'Recover partial sequential fit?', wx.YES \| wx.NO \| wx.CANCEL)
649	dlg.CenterOnParent()
650	try:
651	result = dlg.ShowModal()
652	deleteSeq = result != wx.ID_CANCEL
653	if result == wx.ID_YES:
654	updateFromSeq = True
655	fp = open(GPXphase,'rb')
656	data = cPickleLoad(fp) # first block in file should be Phases
657	if data[0][0] != 'Phases':
658	raise Exception('Unexpected block in {} file. How did this happen?'
659	.format(GPXphase))
660	Phases = {}
661	for name,vals in data[1:]:
662	Phases[name] = vals
663	name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance
664	name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies
665	fp.close()
666	# index the histogram updates
667	hist = open(GPXhist,'rb')
668	try:
669	while True:
670	loc = hist.tell()
671	datum = cPickleLoad(hist)[0]
672	tmpHistIndex[datum[0]] = loc
673	except EOFError:
674	pass
675	finally:
676	dlg.Destroy()
677	wx.BeginBusyCursor()
678	try:
679	while True:
680	try:
681	data = cPickleLoad(filep)
682	except EOFError:
683	break
684	datum = data[0]
685	# scan the GPX file for unexpected objects
686	if GSASIIpath.GetConfigValue('debug'):
687	global unexpectedObject
688	unexpectedObject = False
689	objectScan(data,'tree item "{}" entry '.format(datum[0]))
690	#if unexpectedObject:
691	# print(datum[0])
692	# GSASIIpath.IPyBreak()
693	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
694	if updateFromSeq and datum[0] == 'Phases':
695	for pdata in data[1:]:
696	if pdata[0] in Phases:
697	pdata[1].update(Phases[pdata[0]])
698	elif updateFromSeq and datum[0] == 'Covariance':
699	data[0][1] = CovData
700	elif updateFromSeq and datum[0] == 'Rigid bodies':
701	data[0][1] = RigidBodies
702	elif updateFromSeq and datum[0] in tmpHistIndex:
703	hist.seek(tmpHistIndex[datum[0]])
704	hdata = cPickleLoad(hist)
705	if data[0][0] != hdata[0][0]:
706	print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0]))
707	datum = hdata[0]
708	xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']
709	hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems}
710	for j,(name,val) in enumerate(data[1:]):
711	if name not in xferItems: continue
712	data[j+1][1] = hdata[hItems[name]][1]
713	if datum[0].startswith('PWDR'):
714	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
715	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
716	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
717	elif datum[0].startswith('HKLF'):
718	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
719	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
720	G2frame.GPXtree.SetItemPyData(Id,datum[1])
721	else:
722	G2frame.GPXtree.SetItemPyData(Id,datum[1])
723	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
724	LastSavedUsing = datum[1]['LastSavedUsing']
725	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
726	print('DBG_Packages used to create .GPX file:')
727	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
728	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
729	print(" {:<14s}: {:s}".format(p[0],p[1]))
730	else:
731	for p in datum[1]['PythonVersions']:
732	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
733	oldPDF = False
734	for datus in data[1:]:
735	#patch - 1/23/17 PDF cleanup
736	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
737	oldPDF = True
738	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
739	continue
740	#end PDF cleanup
741	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
742	#patch
743	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
744	if datum[0].startswith('PWDR'):
745	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
746	else:
747	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
748	for item in datus[1][0]: #zip makes tuples - now make lists!
749	datus[1][0][item] = list(datus[1][0][item])
750	#end patch
751	G2frame.GPXtree.SetItemPyData(sub,datus[1])
752	if 'PDF ' in datum[0][:4] and oldPDF:
753	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
754	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
755	if datum [0].startswith('IMG'): #retrieve image default flag & data if set
756	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
757	if Data['setDefault']:
758	G2frame.imageDefault = Data
759	if LastSavedUsing:
760	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
761	else:
762	print('project load successful')
763	G2frame.NewPlot = True
764	except Exception as errmsg:
765	if GSASIIpath.GetConfigValue('debug'):
766	print('\nError reading GPX file:',errmsg)
767	import traceback
768	print (traceback.format_exc())
769	msg = wx.MessageDialog(G2frame,message="Error reading file "+
770	str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
771	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
772	msg.ShowModal()
773	finally:
774	filep.close()
775	wx.EndBusyCursor()
776	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
777	if deleteSeq:
778	if hist: hist.close()
779	try:
780	os.remove(GPXphase)
781	except:
782	print('Warning: unable to delete {}'.format(GPXphase))
783	try:
784	os.remove(GPXhist)
785	except:
786	print('Warning: unable to delete {}'.format(GPXhist))
787	G2frame.SetTitleByGPX()
788
789	def ProjFileSave(G2frame):
790	'Save a GSAS-II project file'
791	if not G2frame.GPXtree.IsEmpty():
792	file = open(G2frame.GSASprojectfile,'wb')
793	print ('save to file: '+G2frame.GSASprojectfile)
794	# stick the file name into the tree and version info into tree so they are saved.
795	# (Controls should always be created at this point)
796	try:
797	Controls = G2frame.GPXtree.GetItemPyData(
798	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
799	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
800	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
801	Controls['PythonVersions'] = G2frame.PackageVersions
802	except:
803	pass
804	wx.BeginBusyCursor()
805	try:
806	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
807	while item:
808	data = []
809	name = G2frame.GPXtree.GetItemText(item)
810	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
811	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
812	while item2:
813	name = G2frame.GPXtree.GetItemText(item2)
814	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
815	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
816	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
817	cPickle.dump(data,file,2)
818	file.close()
819	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
820	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
821	G2frame.LastGPXdir = pth
822	finally:
823	wx.EndBusyCursor()
824	print('project save successful')
825
826	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
827	'Save image integration results as powder pattern(s)'
828	waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
829	'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
830	'Ag':[0.559363,0.563775]}
831	azms = G2frame.Integrate[1]
832	X = G2frame.Integrate[2][:-1]
833	N = len(X)
834	Id = G2frame.GPXtree.GetItemParent(PickId)
835	name = G2frame.GPXtree.GetItemText(Id)
836	name = name.replace('IMG ',data['type']+' ')
837	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
838	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
839	if 'PWDR' in name:
840	if 'target' in data:
841	names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
842	codes = [0 for i in range(14)]
843	else:
844	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
845	codes = [0 for i in range(12)]
846	elif 'SASD' in name:
847	names = ['Type','Lam','Zero','Azimuth']
848	codes = [0 for i in range(4)]
849	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
850	Xminmax = [X[0],X[-1]]
851	Azms = np.zeros(data['outAzimuths'])
852	dazm = 0.
853	if data['outAzimuths'] > 1:
854	dazm = np.min(np.abs(np.diff(azms)))/2.
855	G2frame.IntgOutList = []
856	for i,azm in enumerate(azms[:-1]):
857	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
858	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
859	# if Overwrite delete any duplicate
860	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
861	print('Replacing '+Aname)
862	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
863	G2frame.GPXtree.Delete(item)
864	else:
865	nOcc = 0
866	while item:
867	Name = G2frame.GPXtree.GetItemText(item)
868	if Aname in Name:
869	nOcc += 1
870	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
871	if nOcc:
872	Aname += '(%d)'%(nOcc)
873	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
874	Sample['Gonio. radius'] = data['distance']
875	Sample['Omega'] = data['GonioAngles'][0]
876	Sample['Chi'] = data['GonioAngles'][1]
877	Sample['Phi'] = data['GonioAngles'][2]
878	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
879	polariz = data['PolaVal'][0]
880	for item in Comments:
881	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
882	'Chi','Phi'):
883	if key.lower() in item.lower():
884	try:
885	Sample[key] = float(item.split('=')[1])
886	except:
887	pass
888	if 'label_prm' in item.lower():
889	for num in ('1','2','3'):
890	if 'label_prm'+num in item.lower():
891	Controls['FreePrm'+num] = item.split('=')[1].strip()
892	if 'PWDR' in Aname:
893	if 'target' in data: #from lab x-ray 2D imaging data
894	wave1,wave2 = waves[data['target']]
895	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
896	else:
897	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
898	elif 'SASD' in Aname:
899	Sample['Trans'] = data['SampleAbs'][0]
900	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
901	Y = G2frame.Integrate[0][i]
902	Ymin = np.min(Y)
903	Ymax = np.max(Y)
904	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
905	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
906	G2frame.IntgOutList.append(Id)
907	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
908	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
909	if 'PWDR' in Aname:
910	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
911	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
912	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
913	for item in inst[0]:
914	inst[0][item] = list(inst[0][item])
915	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
916	if 'PWDR' in Aname:
917	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
918	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
919	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
920	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
921	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
922	elif 'SASD' in Aname:
923	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
924	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
925	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
926	valuesdict = {
927	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
928	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
929	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
930	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
931	return Id #last powder pattern generated
932
933	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
934	'Save XY table data'
935	pth = G2G.GetExportPath(G2frame)
936	dlg = wx.FileDialog(
937	G2frame, 'Enter csv filename for XY table', pth, '',
938	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
939	try:
940	if dlg.ShowModal() == wx.ID_OK:
941	filename = dlg.GetPath()
942	filename = os.path.splitext(filename)[0]+'.csv'
943	File = open(filename,'w')
944	else:
945	filename = None
946	finally:
947	dlg.Destroy()
948	if not filename:
949	return
950	for i in range(len(XY)):
951	if len(names):
952	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
953	else:
954	header = '%s,%s(%d)\n'%(labelX,labelY,i)
955	File.write(header)
956	for x,y in XY[i].T:
957	File.write('%.3f,%.3f\n'%(x,y))
958	File.close()
959	print (' XY data saved to: '+filename)
960
961	def PeakListSave(G2frame,file,peaks):
962	'Save powder peaks to a data file'
963	print ('save peak list to file: '+G2frame.peaklistfile)
964	if not peaks:
965	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
966	try:
967	dlg.ShowModal()
968	finally:
969	dlg.Destroy()
970	return
971	for peak in peaks:
972	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
973	(peak[0],peak[2],peak[4],peak[6]))
974	print ('peak list saved')
975
976	def IndexPeakListSave(G2frame,peaks):
977	'Save powder peaks from the indexing list'
978	file = open(G2frame.peaklistfile,'wa')
979	print ('save index peak list to file: '+G2frame.peaklistfile)
980	wx.BeginBusyCursor()
981	try:
982	if not peaks:
983	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
984	try:
985	dlg.ShowModal()
986	finally:
987	dlg.Destroy()
988	return
989	for peak in peaks:
990	file.write("%12.6f\n" % (peak[7]))
991	file.close()
992	finally:
993	wx.EndBusyCursor()
994	print ('index peak list saved')
995
996	def ExtractFileFromZip(filename, selection=None, confirmread=True,
997	confirmoverwrite=True, parent=None,
998	multipleselect=False):
999	'''If the filename is a zip file, extract a file from that
1000	archive.
1001
1002	:param list Selection: used to predefine the name of the file
1003	to be extracted. Filename case and zip directory name are
1004	ignored in selection; the first matching file is used.
1005
1006	:param bool confirmread: if True asks the user to confirm before expanding
1007	the only file in a zip
1008
1009	:param bool confirmoverwrite: if True asks the user to confirm
1010	before overwriting if the extracted file already exists
1011
1012	:param bool multipleselect: if True allows more than one zip
1013	file to be extracted, a list of file(s) is returned.
1014	If only one file is present, do not ask which one, otherwise
1015	offer a list of choices (unless selection is used).
1016
1017	:returns: the name of the file that has been created or a
1018	list of files (see multipleselect)
1019
1020	If the file is not a zipfile, return the name of the input file.
1021	If the zipfile is empty or no file has been selected, return None
1022	'''
1023	import zipfile # do this now, since we can save startup time by doing this only on need
1024	import shutil
1025	zloc = os.path.split(filename)[0]
1026	if not zipfile.is_zipfile(filename):
1027	#print("not zip")
1028	return filename
1029
1030	z = zipfile.ZipFile(filename,'r')
1031	zinfo = z.infolist()
1032
1033	if len(zinfo) == 0:
1034	#print('Zip has no files!')
1035	zlist = [-1]
1036	if selection:
1037	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1038	if selection.lower() in choices:
1039	zlist = [choices.index(selection.lower())]
1040	else:
1041	print('debug: file '+str(selection)+' was not found in '+str(filename))
1042	zlist = [-1]
1043	elif len(zinfo) == 1 and confirmread:
1044	result = wx.ID_NO
1045	dlg = wx.MessageDialog(
1046	parent,
1047	'Is file '+str(zinfo[0].filename)+
1048	' what you want to extract from '+
1049	str(os.path.split(filename)[1])+'?',
1050	'Confirm file',
1051	wx.YES_NO \| wx.ICON_QUESTION)
1052	try:
1053	result = dlg.ShowModal()
1054	finally:
1055	dlg.Destroy()
1056	if result == wx.ID_NO:
1057	zlist = [-1]
1058	else:
1059	zlist = [0]
1060	elif len(zinfo) == 1:
1061	zlist = [0]
1062	elif multipleselect:
1063	# select one or more from a from list
1064	choices = [i.filename for i in zinfo]
1065	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1066	'Choose file(s)',choices)
1067	if dlg.ShowModal() == wx.ID_OK:
1068	zlist = dlg.GetSelections()
1069	else:
1070	zlist = []
1071	dlg.Destroy()
1072	else:
1073	# select one from a from list
1074	choices = [i.filename for i in zinfo]
1075	dlg = wx.SingleChoiceDialog(parent,
1076	'Select file to extract from zip file'+str(filename),'Choose file',
1077	choices,)
1078	if dlg.ShowModal() == wx.ID_OK:
1079	zlist = [dlg.GetSelection()]
1080	else:
1081	zlist = [-1]
1082	dlg.Destroy()
1083
1084	outlist = []
1085	for zindex in zlist:
1086	if zindex >= 0:
1087	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1088	if os.path.exists(efil) and confirmoverwrite:
1089	result = wx.ID_NO
1090	dlg = wx.MessageDialog(parent,
1091	'File '+str(efil)+' already exists. OK to overwrite it?',
1092	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1093	try:
1094	result = dlg.ShowModal()
1095	finally:
1096	dlg.Destroy()
1097	if result == wx.ID_NO:
1098	zindex = -1
1099	if zindex >= 0:
1100	# extract the file to the current directory, regardless of it's original path
1101	#z.extract(zinfo[zindex],zloc)
1102	eloc,efil = os.path.split(zinfo[zindex].filename)
1103	outfile = os.path.join(zloc, efil)
1104	fpin = z.open(zinfo[zindex])
1105	fpout = open(outfile, "wb")
1106	shutil.copyfileobj(fpin, fpout)
1107	fpin.close()
1108	fpout.close()
1109	outlist.append(outfile)
1110	z.close()
1111	if multipleselect and len(outlist) >= 1:
1112	return outlist
1113	elif len(outlist) == 1:
1114	return outlist[0]
1115	else:
1116	return None
1117
1118	def striphist(var,insChar=''):
1119	'strip a histogram number from a var name'
1120	sv = var.split(':')
1121	if len(sv) <= 1: return var
1122	if sv[1]:
1123	sv[1] = insChar
1124	return ':'.join(sv)
1125
1126	######################################################################
1127	# base classes for reading various types of data files
1128	# not used directly, only by subclassing
1129	######################################################################
1130	class ExportBaseclass(object):
1131	'''Defines a base class for the exporting of GSAS-II results.
1132
1133	This class is subclassed in the various exports/G2export_*.py files. Those files
1134	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1135	appropriate menu items for each one and the .Exporter method is called
1136	directly from the menu item.
1137
1138	Routines may also define a .Writer method, which is used to write a single
1139	file without invoking any GUI objects.
1140	'''
1141	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1142	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1143	# TODO: move this class to G2fil
1144	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1145	self.G2frame = G2frame
1146	self.formatName = formatName # short string naming file type
1147	self.extension = extension
1148	if longFormatName: # longer string naming file type
1149	self.longFormatName = longFormatName
1150	else:
1151	self.longFormatName = formatName
1152	self.OverallParms = {}
1153	self.Phases = {}
1154	self.Histograms = {}
1155	self.powderDict = {}
1156	self.sasdDict = {}
1157	self.refdDict = {}
1158	self.xtalDict = {}
1159	self.parmDict = {}
1160	self.sigDict = {}
1161	self.fp = None
1162	# updated in InitExport:
1163	self.currentExportType = None # type of export that has been requested
1164	# updated in ExportSelect (when used):
1165	self.phasenam = None # a list of selected phases
1166	self.histnam = None # a list of selected histograms
1167	self.filename = None # name of file to be written (single export) or template (multiple files)
1168	self.dirname = '' # name of directory where file(s) will be written
1169	self.fullpath = '' # name of file being written -- full path
1170
1171	# items that should be defined in a subclass of this class
1172	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1173	# The following types are defined: 'project', "phase", "powder", "single"
1174	self.multiple = False # set as True if the class can export multiple phases or histograms
1175	# self.multiple is ignored for "project" exports
1176
1177	def InitExport(self,event):
1178	'''Determines the type of menu that called the Exporter and
1179	misc initialization.
1180	'''
1181	self.filename = None # name of file to be written (single export)
1182	self.dirname = '' # name of file to be written (multiple export)
1183	if event:
1184	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1185
1186	def MakePWDRfilename(self,hist):
1187	'''Make a filename root (no extension) from a PWDR histogram name
1188
1189	:param str hist: the histogram name in data tree (starts with "PWDR ")
1190	'''
1191	file0 = ''
1192	file1 = hist[5:]
1193	# replace repeated blanks
1194	while file1 != file0:
1195	file0 = file1
1196	file1 = file0.replace(' ',' ').strip()
1197	file0 = file1.replace('Azm= ','A')
1198	# if angle has unneeded decimal places on aziumuth, remove them
1199	if file0[-3:] == '.00': file0 = file0[:-3]
1200	file0 = file0.replace('.','_')
1201	file0 = file0.replace(' ','_')
1202	return file0
1203
1204	def ExportSelect(self,AskFile='ask'):
1205	'''Selects histograms or phases when needed. Sets a default file name when
1206	requested into self.filename; always sets a default directory in self.dirname.
1207
1208	:param bool AskFile: Determines how this routine processes getting a
1209	location to store the current export(s).
1210
1211	* if AskFile is 'ask' (default option), get the name of the file to be written;
1212	self.filename and self.dirname are always set. In the case where
1213	multiple files must be generated, the export routine should do this
1214	based on self.filename as a template.
1215	* if AskFile is 'dir', get the name of the directory to be used;
1216	self.filename is not used, but self.dirname is always set. The export routine
1217	will always generate the file name.
1218	* if AskFile is 'single', get only the name of the directory to be used when
1219	multiple items will be written (as multiple files) are used
1220	or a complete file name is requested when a single file
1221	name is selected. self.dirname is always set and self.filename used
1222	only when a single file is selected.
1223	* if AskFile is 'default', creates a name of the file to be used from
1224	the name of the project (.gpx) file. If the project has not been saved,
1225	then the name of file is requested.
1226	self.filename and self.dirname are always set. In the case where
1227	multiple file names must be generated, the export routine should do this
1228	based on self.filename.
1229	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1230	file. If the project has not been saved, then a directory is requested.
1231	self.filename is not used.
1232
1233	:returns: True in case of an error
1234	'''
1235
1236	numselected = 1
1237	if self.currentExportType == 'phase':
1238	if len(self.Phases) == 0:
1239	self.G2frame.ErrorDialog(
1240	'Empty project',
1241	'Project does not contain any phases.')
1242	return True
1243	elif len(self.Phases) == 1:
1244	self.phasenam = list(self.Phases.keys())
1245	elif self.multiple:
1246	choices = sorted(self.Phases.keys())
1247	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1248	if phasenum is None: return True
1249	self.phasenam = [choices[i] for i in phasenum]
1250	if not self.phasenam: return True
1251	numselected = len(self.phasenam)
1252	else:
1253	choices = sorted(self.Phases.keys())
1254	phasenum = G2G.ItemSelector(choices,self.G2frame)
1255	if phasenum is None: return True
1256	self.phasenam = [choices[phasenum]]
1257	numselected = len(self.phasenam)
1258	elif self.currentExportType == 'single':
1259	if len(self.xtalDict) == 0:
1260	self.G2frame.ErrorDialog(
1261	'Empty project',
1262	'Project does not contain any single crystal data.')
1263	return True
1264	elif len(self.xtalDict) == 1:
1265	self.histnam = self.xtalDict.values()
1266	elif self.multiple:
1267	choices = sorted(self.xtalDict.values())
1268	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1269	if not hnum: return True
1270	self.histnam = [choices[i] for i in hnum]
1271	numselected = len(self.histnam)
1272	else:
1273	choices = sorted(self.xtalDict.values())
1274	hnum = G2G.ItemSelector(choices,self.G2frame)
1275	if hnum is None: return True
1276	self.histnam = [choices[hnum]]
1277	numselected = len(self.histnam)
1278	elif self.currentExportType == 'powder':
1279	if len(self.powderDict) == 0:
1280	self.G2frame.ErrorDialog(
1281	'Empty project',
1282	'Project does not contain any powder data.')
1283	return True
1284	elif len(self.powderDict) == 1:
1285	self.histnam = list(self.powderDict.values())
1286	elif self.multiple:
1287	choices = sorted(self.powderDict.values())
1288	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1289	if not hnum: return True
1290	self.histnam = [choices[i] for i in hnum]
1291	numselected = len(self.histnam)
1292	else:
1293	choices = sorted(self.powderDict.values())
1294	hnum = G2G.ItemSelector(choices,self.G2frame)
1295	if hnum is None: return True
1296	self.histnam = [choices[hnum]]
1297	numselected = len(self.histnam)
1298	elif self.currentExportType == 'sasd':
1299	if len(self.sasdDict) == 0:
1300	self.G2frame.ErrorDialog(
1301	'Empty project',
1302	'Project does not contain any small angle data.')
1303	return True
1304	elif len(self.sasdDict) == 1:
1305	self.histnam = self.sasdDict.values()
1306	elif self.multiple:
1307	choices = sorted(self.sasdDict.values())
1308	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1309	if not hnum: return True
1310	self.histnam = [choices[i] for i in hnum]
1311	numselected = len(self.histnam)
1312	else:
1313	choices = sorted(self.sasdDict.values())
1314	hnum = G2G.ItemSelector(choices,self.G2frame)
1315	if hnum is None: return True
1316	self.histnam = [choices[hnum]]
1317	numselected = len(self.histnam)
1318	elif self.currentExportType == 'refd':
1319	if len(self.refdDict) == 0:
1320	self.G2frame.ErrorDialog(
1321	'Empty project',
1322	'Project does not contain any reflectivity data.')
1323	return True
1324	elif len(self.refdDict) == 1:
1325	self.histnam = self.refdDict.values()
1326	elif self.multiple:
1327	choices = sorted(self.refdDict.values())
1328	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1329	if not hnum: return True
1330	self.histnam = [choices[i] for i in hnum]
1331	numselected = len(self.histnam)
1332	else:
1333	choices = sorted(self.refdDict.values())
1334	hnum = G2G.ItemSelector(choices,self.G2frame)
1335	if hnum is None: return True
1336	self.histnam = [choices[hnum]]
1337	numselected = len(self.histnam)
1338	elif self.currentExportType == 'image':
1339	if len(self.Histograms) == 0:
1340	self.G2frame.ErrorDialog(
1341	'Empty project',
1342	'Project does not contain any images.')
1343	return True
1344	elif len(self.Histograms) == 1:
1345	self.histnam = list(self.Histograms.keys())
1346	else:
1347	choices = sorted(self.Histograms.keys())
1348	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1349	if self.multiple:
1350	if not hnum: return True
1351	self.histnam = [choices[i] for i in hnum]
1352	else:
1353	if hnum is None: return True
1354	self.histnam = [choices[hnum]]
1355	numselected = len(self.histnam)
1356	if self.currentExportType == 'map':
1357	# search for phases with maps
1358	mapPhases = []
1359	choices = []
1360	for phasenam in sorted(self.Phases):
1361	phasedict = self.Phases[phasenam] # pointer to current phase info
1362	if len(phasedict['General']['Map'].get('rho',[])):
1363	mapPhases.append(phasenam)
1364	if phasedict['General']['Map'].get('Flip'):
1365	choices.append('Charge flip map: '+str(phasenam))
1366	elif phasedict['General']['Map'].get('MapType'):
1367	choices.append(
1368	str(phasedict['General']['Map'].get('MapType'))
1369	+ ' map: ' + str(phasenam))
1370	else:
1371	choices.append('unknown map: '+str(phasenam))
1372	# select a map if needed
1373	if len(mapPhases) == 0:
1374	self.G2frame.ErrorDialog(
1375	'Empty project',
1376	'Project does not contain any maps.')
1377	return True
1378	elif len(mapPhases) == 1:
1379	self.phasenam = mapPhases
1380	else:
1381	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1382	if self.multiple:
1383	if not phasenum: return True
1384	self.phasenam = [mapPhases[i] for i in phasenum]
1385	else:
1386	if phasenum is None: return True
1387	self.phasenam = [mapPhases[phasenum]]
1388	numselected = len(self.phasenam)
1389
1390	# items selected, now set self.dirname and usually self.filename
1391	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1392	AskFile == 'default' and not self.G2frame.GSASprojectfile
1393	):
1394	filename = self.askSaveFile()
1395	if not filename: return True
1396	self.dirname,self.filename = os.path.split(filename)
1397	elif AskFile == 'dir' or AskFile == 'single' or (
1398	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1399	):
1400	self.dirname = self.askSaveDirectory()
1401	if not self.dirname: return True
1402	elif AskFile == 'default-dir' or AskFile == 'default':
1403	self.dirname,self.filename = os.path.split(
1404	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1405	)
1406	else:
1407	raise Exception('This should not happen!')
1408
1409	def loadParmDict(self):
1410	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1411	refined values to those from the last cycle and set the uncertainties for the
1412	refined parameters in another dict (self.sigDict).
1413
1414	Expands the parm & sig dicts to include values derived from constraints.
1415
1416	This could be made faster for sequential fits by reducing the histogram list to only
1417	the active histogram being exported.
1418	'''
1419	self.G2frame.CheckNotebook()
1420	self.parmDict = {}
1421	self.sigDict = {}
1422	rigidbodyDict = {}
1423	covDict = {}
1424	consDict = {}
1425	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1426	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1427	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1428	while item:
1429	name = self.G2frame.GPXtree.GetItemText(item)
1430	if name == 'Rigid bodies':
1431	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1432	elif name == 'Covariance':
1433	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1434	elif name == 'Constraints':
1435	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1436	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1437	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1438	self.parmDict.update(rbDict)
1439	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1440	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1441	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1442	self.parmDict.update(phaseDict)
1443	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1444	Phases,Histograms,Print=False,resetRefList=False)
1445	self.parmDict.update(hapDict)
1446	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1447	self.parmDict.update(histDict)
1448	self.parmDict.update(zip(
1449	covDict.get('varyList',[]),
1450	covDict.get('variables',[])))
1451	self.sigDict = dict(zip(
1452	covDict.get('varyList',[]),
1453	covDict.get('sig',[])))
1454	# expand to include constraints: first compile a list of constraints
1455	constList = []
1456	for item in consDict:
1457	if item.startswith('_'): continue
1458	constList += consDict[item]
1459	# now process the constraints
1460	G2mv.InitVars()
1461	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1462	varyList = covDict.get('varyListStart')
1463	if varyList is None and len(constDict) == 0:
1464	# no constraints can use varyList
1465	varyList = covDict.get('varyList')
1466	elif varyList is None:
1467	# old GPX file from before pre-constraint varyList is saved
1468	print (' * Old refinement: Please use Calculate/Refine to redo *')
1469	raise Exception(' * Export aborted *')
1470	else:
1471	varyList = list(varyList)
1472	# add symmetry-generated constraints
1473	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1474	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1475	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1476	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1477	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1478	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1479	msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1480	if msg:
1481	print('Unable to interpret multiplier(s): '+msg)
1482	raise Exception(' * CIF creation aborted *')
1483	try:
1484	G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1485	#print(G2mv.VarRemapShow(varyList))
1486	except:
1487	# this really should not happen
1488	print (' * ERROR - constraints are internally inconsistent *')
1489	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1490	print ('Errors'+errmsg)
1491	if warnmsg: print ('Warnings'+warnmsg)
1492	raise Exception(' * CIF creation aborted *')
1493	# add the constrained values to the parameter dictionary
1494	G2mv.Dict2Map(self.parmDict,varyList)
1495	# and add their uncertainties into the esd dictionary (sigDict)
1496	if covDict.get('covMatrix') is not None:
1497	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1498
1499	def loadTree(self):
1500	'''Load the contents of the data tree into a set of dicts
1501	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1502	& self.xtalDict)
1503
1504	* The childrenless data tree items are overall parameters/controls for the
1505	entire project and are placed in self.OverallParms
1506	* Phase items are placed in self.Phases
1507	* Data items are placed in self.Histogram. The key for these data items
1508	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1509	'''
1510	self.OverallParms = {}
1511	self.powderDict = {}
1512	self.sasdDict = {}
1513	self.refdDict = {}
1514	self.xtalDict = {}
1515	self.Phases = {}
1516	self.Histograms = {}
1517	self.SeqRefdata = None
1518	self.SeqRefhist = None
1519	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1520	histType = None
1521	if self.currentExportType == 'phase':
1522	# if exporting phases load them here
1523	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1524	if not sub:
1525	print ('no phases found')
1526	return True
1527	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1528	while item:
1529	phaseName = self.G2frame.GPXtree.GetItemText(item)
1530	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1531	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1532	return
1533	elif self.currentExportType == 'single':
1534	histType = 'HKLF'
1535	elif self.currentExportType == 'powder':
1536	histType = 'PWDR'
1537	elif self.currentExportType == 'image':
1538	histType = 'IMG'
1539	elif self.currentExportType == 'sasd':
1540	histType = 'SASD'
1541	elif self.currentExportType == 'refd':
1542	histType = 'REFD'
1543
1544	if histType: # Loading just one kind of tree entry
1545	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1546	while item:
1547	name = self.G2frame.GPXtree.GetItemText(item)
1548	if name.startswith(histType):
1549	if self.Histograms.get(name): # there is already an item with this name
1550	print('Histogram name '+str(name)+' is repeated. Renaming')
1551	if name[-1] == '9':
1552	name = name[:-1] + '10'
1553	elif name[-1] in '012345678':
1554	name = name[:-1] + str(int(name[-1])+1)
1555	else:
1556	name += '-1'
1557	self.Histograms[name] = {}
1558	# the main info goes into Data, but the 0th
1559	# element contains refinement results, carry
1560	# that over too now.
1561	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1562	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1563	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1564	while item2:
1565	child = self.G2frame.GPXtree.GetItemText(item2)
1566	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1567	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1568	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1569	# index powder and single crystal histograms by number
1570	for hist in self.Histograms:
1571	if hist.startswith("PWDR"):
1572	d = self.powderDict
1573	elif hist.startswith("HKLF"):
1574	d = self.xtalDict
1575	elif hist.startswith("SASD"):
1576	d = self.sasdDict
1577	elif hist.startswith("REFD"):
1578	d = self.refdDict
1579	else:
1580	return
1581	i = self.Histograms[hist].get('hId')
1582	if i is None and not d.keys():
1583	i = 0
1584	elif i is None or i in d.keys():
1585	i = max(d.keys())+1
1586	d[i] = hist
1587	return
1588	# else standard load: using all interlinked phases and histograms
1589	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1590	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1591	while item:
1592	name = self.G2frame.GPXtree.GetItemText(item)
1593	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1594	if not item2:
1595	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1596	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1597	# index powder and single crystal histograms
1598	for hist in self.Histograms:
1599	i = self.Histograms[hist]['hId']
1600	if hist.startswith("PWDR"):
1601	self.powderDict[i] = hist
1602	elif hist.startswith("HKLF"):
1603	self.xtalDict[i] = hist
1604	elif hist.startswith("SASD"):
1605	self.sasdDict[i] = hist
1606	elif hist.startswith("REFD"):
1607	self.refdDict[i] = hist
1608
1609	def dumpTree(self,mode='type'):
1610	'''Print out information on the data tree dicts loaded in loadTree.
1611	Used for testing only.
1612	'''
1613	if self.SeqRefdata and self.SeqRefhist:
1614	print('Note that dumpTree does not show sequential results')
1615	print ('\nOverall')
1616	if mode == 'type':
1617	def Show(arg): return type(arg)
1618	else:
1619	def Show(arg): return arg
1620	for key in self.OverallParms:
1621	print (' '+key+Show(self.OverallParms[key]))
1622	print ('Phases')
1623	for key1 in self.Phases:
1624	print (' '+key1+Show(self.Phases[key1]))
1625	print ('Histogram')
1626	for key1 in self.Histograms:
1627	print (' '+key1+Show(self.Histograms[key1]))
1628	for key2 in self.Histograms[key1]:
1629	print (' '+key2+Show(self.Histograms[key1][key2]))
1630
1631	def defaultSaveFile(self):
1632	return os.path.abspath(
1633	os.path.splitext(self.G2frame.GSASprojectfile
1634	)[0]+self.extension)
1635
1636	def askSaveFile(self):
1637	'''Ask the user to supply a file name
1638
1639	:returns: a file name (str) or None if Cancel is pressed
1640
1641	'''
1642	#pth = G2G.GetExportPath(self.G2frame)
1643	if self.G2frame.GSASprojectfile:
1644	defnam = os.path.splitext(
1645	os.path.split(self.G2frame.GSASprojectfile)[1]
1646	)[0]+self.extension
1647	else:
1648	defnam = 'default' + self.extension
1649	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1650
1651	def askSaveDirectory(self):
1652	'''Ask the user to supply a directory name. Path name is used as the
1653	starting point for the next export path search.
1654
1655	:returns: a directory name (str) or None if Cancel is pressed
1656
1657	TODO: Can this be replaced with G2G.askSaveDirectory?
1658	'''
1659	pth = G2G.GetExportPath(self.G2frame)
1660	dlg = wx.DirDialog(
1661	self.G2frame, 'Input directory where file(s) will be written', pth,
1662	wx.DD_DEFAULT_STYLE)
1663	dlg.CenterOnParent()
1664	try:
1665	if dlg.ShowModal() == wx.ID_OK:
1666	filename = dlg.GetPath()
1667	self.G2frame.LastExportDir = filename
1668	else:
1669	filename = None
1670	finally:
1671	dlg.Destroy()
1672	return filename
1673
1674	# Tools for file writing.
1675	def OpenFile(self,fil=None,mode='w'):
1676	'''Open the output file
1677
1678	:param str fil: The name of the file to open. If None (default)
1679	the name defaults to self.dirname + self.filename.
1680	If an extension is supplied, it is not overridded,
1681	but if not, the default extension is used.
1682	:returns: the file object opened by the routine which is also
1683	saved as self.fp
1684	'''
1685	if mode == 'd': # debug mode
1686	self.fullpath = '(stdout)'
1687	self.fp = sys.stdout
1688	return
1689	if not fil:
1690	if not os.path.splitext(self.filename)[1]:
1691	self.filename += self.extension
1692	fil = os.path.join(self.dirname,self.filename)
1693	self.fullpath = os.path.abspath(fil)
1694	self.fp = open(self.fullpath,mode)
1695	return self.fp
1696
1697	def Write(self,line):
1698	'''write a line of output, attaching a line-end character
1699
1700	:param str line: the text to be written.
1701	'''
1702	if self.fp is None:
1703	raise Exception('Attempt to Write without use of OpenFile')
1704	self.fp.write(line+'\n')
1705
1706	def CloseFile(self,fp=None):
1707	'''Close a file opened in OpenFile
1708
1709	:param file fp: the file object to be closed. If None (default)
1710	file object self.fp is closed.
1711	'''
1712	if self.fp is None:
1713	raise Exception('Attempt to CloseFile without use of OpenFile')
1714	if self.fp == sys.stdout: return # debug mode
1715	if fp is None:
1716	fp = self.fp
1717	self.fp = None
1718	if fp is not None: fp.close()
1719
1720	def SetSeqRef(self,data,hist):
1721	'''Set the exporter to retrieve results from a sequential refinement
1722	rather than the main tree
1723	'''
1724	self.SeqRefdata = data
1725	self.SeqRefhist = hist
1726	data_name = data[hist]
1727	for i,val in zip(data_name['varyList'],data_name['sig']):
1728	self.sigDict[i] = val
1729	self.sigDict[striphist(i)] = val
1730	for i in data_name['parmDict']:
1731	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1732	self.parmDict[i] = data_name['parmDict'][i]
1733	# zero out the dA[xyz] terms, they would only bring confusion
1734	key = i.split(':')
1735	if len(key) < 3: continue
1736	if key[2].startswith('dA'):
1737	self.parmDict[i] = 0.0
1738	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1739	self.parmDict[i] = val
1740	self.sigDict[i] = sig
1741	#GSASIIpath.IPyBreak()
1742
1743	# Tools to pull information out of the data arrays
1744	def GetCell(self,phasenam):
1745	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1746
1747	:param str phasenam: the name for the selected phase
1748	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1749	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1750	cell values and `cellSig` has their uncertainties.
1751	"""
1752	if self.SeqRefdata and self.SeqRefhist:
1753	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1754	phasedict = self.Phases[phasenam] # pointer to current phase info
1755	try:
1756	pfx = str(phasedict['pId'])+'::'
1757	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1758	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1759	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1760	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1761	return cellList,cellSig
1762	except KeyError:
1763	cell = phasedict['General']['Cell'][1:]
1764	return cell,7*[0]
1765
1766	def GetSeqCell(self,phasenam,data_name):
1767	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1768	and histogram in a sequential fit
1769
1770	:param str phasenam: the name for the selected phase
1771	:param dict data_name: the sequential refinement parameters for the selected histogram
1772	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1773	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1774	cell values and `cellSig` has their uncertainties.
1775	"""
1776	phasedict = self.Phases[phasenam]
1777	SGdata = phasedict['General']['SGData']
1778	pId = phasedict['pId']
1779	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1780	ESDlookup = {}
1781	Dlookup = {}
1782	varied = [striphist(i) for i in data_name['varyList']]
1783	for item,val in data_name['newCellDict'].items():
1784	if item in varied:
1785	ESDlookup[val[0]] = item
1786	Dlookup[item] = val[0]
1787	A = RecpCellTerms[:]
1788	for i in range(6):
1789	var = str(pId)+'::A'+str(i)
1790	if var in ESDlookup:
1791	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1792	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1793	zeroDict = {i:0.0 for i in cellDict}
1794	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1795	covData = {
1796	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1797	'covMatrix': data_name['covMatrix']
1798	}
1799	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1800
1801	def GetAtoms(self,phasenam):
1802	"""Gets the atoms associated with a phase. Can be used with standard
1803	or macromolecular phases
1804
1805	:param str phasenam: the name for the selected phase
1806	:returns: a list of items for eac atom where each item is a list containing:
1807	label, typ, mult, xyz, and td, where
1808
1809	* label and typ are the atom label and the scattering factor type (str)
1810	* mult is the site multiplicity (int)
1811	* xyz is contains a list with four pairs of numbers:
1812	x, y, z and fractional occupancy and
1813	their standard uncertainty (or a negative value)
1814	* td is contains a list with either one or six pairs of numbers:
1815	if one number it is U\ :sub:`iso` and with six numbers it is
1816	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1817	paired with their standard uncertainty (or a negative value)
1818	"""
1819	phasedict = self.Phases[phasenam] # pointer to current phase info
1820	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1821	cfrac = cx+3
1822	fpfx = str(phasedict['pId'])+'::Afrac:'
1823	atomslist = []
1824	for i,at in enumerate(phasedict['Atoms']):
1825	if phasedict['General']['Type'] == 'macromolecular':
1826	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1827	else:
1828	label = at[ct-1]
1829	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1830	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1831	mult = at[cs+1]
1832	typ = at[ct]
1833	xyz = []
1834	for j,v in enumerate(('x','y','z')):
1835	val = at[cx+j]
1836	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1837	val = self.parmDict.get(pfx, val)
1838	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1839	sig = self.sigDict.get(dpfx,-0.000009)
1840	xyz.append((val,sig))
1841	xyz.append((fval,fsig))
1842	td = []
1843	if at[cia] == 'I':
1844	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1845	val = self.parmDict.get(pfx,at[cia+1])
1846	sig = self.sigDict.get(pfx,-0.0009)
1847	td.append((val,sig))
1848	else:
1849	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1850	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1851	val = self.parmDict.get(pfx,at[cia+2+i])
1852	sig = self.sigDict.get(pfx,-0.0009)
1853	td.append((val,sig))
1854	atomslist.append((label,typ,mult,xyz,td))
1855	return atomslist
1856	######################################################################
1857	def ExportPowderList(G2frame):
1858	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1859	along with their descriptions (note that a extension may be repeated
1860	but descriptions are unique).
1861	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1862
1863	:param wx.Frame G2frame: the GSAS-II main data tree window
1864	'''
1865	extList = []
1866	extLabel = []
1867	for obj in G2frame.exporterlist:
1868	if 'powder' in obj.exporttype:
1869	try:
1870	obj.Writer
1871	extList.append(obj.extension)
1872	extLabel.append(obj.formatName)
1873	except AttributeError:
1874	pass
1875	return extList,extLabel
1876
1877	def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1878	'''Writes a single powder histogram using the Export routines.
1879	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1880
1881	:param wx.Frame G2frame: the GSAS-II main data tree window
1882	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1883	:param str fileroot: name for file to be written, extension ignored
1884	:param str extension: extension for file to be written (start with '.'). Must
1885	match a powder export routine that has a Writer object.
1886	:param str hint: a string that must match the export's format
1887	'''
1888	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1889	for obj in G2frame.exporterlist:
1890	if obj.extension == extension and 'powder' in obj.exporttype:
1891	if hint and hint not in obj.formatName: continue
1892	obj.currentExportType = 'powder'
1893	obj.InitExport(None)
1894	obj.loadTree() # load all histograms in tree into dicts
1895	if TreeName not in obj.Histograms:
1896	raise Exception('Histogram not found: '+str(TreeName))
1897	try:
1898	obj.Writer
1899	except AttributeError:
1900	continue
1901	try:
1902	obj.Writer(TreeName,filename)
1903	print('wrote file '+filename)
1904	return
1905	except Exception:
1906	print('Export Routine for '+extension+' failed.')
1907	else:
1908	print('No Export routine supports extension '+extension)
1909
1910	def ExportSequential(G2frame,data,obj,exporttype):
1911	'''
1912	Used to export from every phase/dataset in a sequential refinement using
1913	a .Writer method for either projects or phases. Prompts to select histograms
1914	and for phase exports, which phase(s).
1915
1916	:param wx.Frame G2frame: the GSAS-II main data tree window
1917	:param dict data: the sequential refinement data object
1918	:param str exporttype: indicates the type of export ('project' or 'phase')
1919	'''
1920	if len(data['histNames']) == 0:
1921	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1922	obj.InitExport(None)
1923	obj.loadTree()
1924	obj.loadParmDict()
1925	if len(data['histNames']) == 1:
1926	histlist = data['histNames']
1927	else:
1928	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1929	'Select histograms',data['histNames'])
1930	if dlg.ShowModal() == wx.ID_OK:
1931	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1932	dlg.Destroy()
1933	else:
1934	dlg.Destroy()
1935	return
1936	if exporttype == 'Phase':
1937	phaselist = list(obj.Phases.keys())
1938	if len(obj.Phases) == 0:
1939	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1940	return
1941	elif len(obj.Phases) > 1:
1942	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1943	'Select phases', phaselist)
1944	if dlg.ShowModal() == wx.ID_OK:
1945	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1946	dlg.Destroy()
1947	else:
1948	dlg.Destroy()
1949	return
1950	filename = obj.askSaveFile()
1951	if not filename: return True
1952	obj.dirname,obj.filename = os.path.split(filename)
1953	print('Writing output to file '+str(obj.filename)+"...")
1954	mode = 'w'
1955	for p in phaselist:
1956	for h in histlist:
1957	obj.SetSeqRef(data,h)
1958	#GSASIIpath.IPyBreak()
1959	obj.Writer(h,phasenam=p,mode=mode)
1960	mode = 'a'
1961	print('...done')
1962	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
1963	filename = obj.askSaveFile()
1964	if not filename: return True
1965	obj.dirname,obj.filename = os.path.split(filename)
1966	print('Writing output to file '+str(obj.filename)+"...")
1967	mode = 'w'
1968	for h in histlist:
1969	obj.SetSeqRef(data,h)
1970	obj.Writer(h,mode=mode)
1971	print('\t'+str(h)+' written')
1972	mode = 'a'
1973	print('...done')
1974	elif exporttype == 'Powder':
1975	filename = obj.askSaveFile()
1976	if not filename: return True
1977	obj.dirname,obj.filename = os.path.split(filename)
1978	print('Writing output to file '+str(obj.filename)+"...")
1979	mode = 'w'
1980	for h in histlist:
1981	obj.SetSeqRef(data,h)
1982	obj.Writer(h,mode=mode)
1983	print('\t'+str(h)+' written')
1984	mode = 'a'
1985	print('...done')
1986
1987	def ReadDIFFaX(DIFFaXfile):
1988	print ('read '+DIFFaXfile)
1989	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
1990	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
1991	df = open(DIFFaXfile,'r')
1992	lines = df.readlines()
1993	df.close()
1994	struct = False
1995	Struct = []
1996	stack = False
1997	Stack = []
1998	trans = False
1999	Trans = []
2000	for diff in lines:
2001	diff = diff[:-1].lower()
2002	if '!' in diff:
2003	continue
2004	while '}' in diff: #strip comments
2005	iB = diff.index('{')
2006	iF = diff.index('}')+1
2007	if iB:
2008	diff = diff[:iB]
2009	else:
2010	diff = diff[iF:]
2011	if not diff:
2012	continue
2013	if diff.strip() == 'instrumental':
2014	continue
2015	if diff.strip() == 'structural':
2016	struct = True
2017	continue
2018	elif diff.strip() == 'stacking':
2019	struct = False
2020	stack = True
2021	continue
2022	elif diff.strip() == 'transitions':
2023	stack = False
2024	trans = True
2025	continue
2026	diff = diff.strip()
2027	if struct:
2028	if diff:
2029	Struct.append(diff)
2030	elif stack:
2031	if diff:
2032	Stack.append(diff)
2033	elif trans:
2034	if diff:
2035	Trans.append(diff)
2036
2037	#STRUCTURE records
2038	laueRec = Struct[1].split()
2039	Layer['Laue'] = laueRec[0]
2040	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2041	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2042	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2043	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2044	cell = Struct[0].split()
2045	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2046	nLayers = int(Struct[2])
2047	N = 3
2048	if 'layer' not in Struct[3]:
2049	N = 4
2050	if Struct[3] != 'infinite':
2051	width = Struct[3].split()
2052	Layer['Width'][0] = [float(width[0]),float(width[1])]
2053	for nL in range(nLayers):
2054	if '=' in Struct[N]:
2055	name = Struct[N].split('=')
2056	sameas = int(name[1])-1
2057	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2058	N += 1
2059	continue
2060	Symm = 'None'
2061	if 'centro' in Struct[N+1]: Symm = '-1'
2062	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2063	N += 2
2064	while 'layer' not in Struct[N]:
2065	atom = Struct[N][4:].split()
2066	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2067	if atomType not in Layer['AtInfo']:
2068	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2069	atomName = '%s(%s)'%(atomType,atom[0])
2070	newVals = []
2071	for val in atom[1:6]:
2072	if '/' in val:
2073	newVals.append(eval(val+'.'))
2074	else:
2075	newVals.append(float(val))
2076	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2077	Layer['Layers'][-1]['Atoms'].append(atomRec)
2078	N += 1
2079	if N > len(Struct)-1:
2080	break
2081	#TRANSITIONS records
2082	transArray = []
2083	N = 0
2084	for i in range(nLayers):
2085	transArray.append([])
2086	for j in range(nLayers):
2087	vals = Trans[N].split()
2088	newVals = []
2089	for val in vals[:4]:
2090	if '/' in val:
2091	newVals.append(eval(val+'.'))
2092	else:
2093	newVals.append(float(val))
2094	transArray[-1].append(newVals+['',False])
2095	N += 1
2096	Layer['Transitions'] = transArray
2097	#STACKING records
2098	Layer['Stacking'] = [Stack[0],'']
2099	if Stack[0] == 'recursive':
2100	Layer['Stacking'][1] = Stack[1]
2101	elif Stack[0] == 'explicit':
2102	if Stack[1] == 'random':
2103	Layer['Stacking'][1] = Stack[1]
2104	else:
2105	Layer['Stacking'][1] = 'list'
2106	Layer['Stacking'].append('')
2107	for stack in Stack[2:]:
2108	Layer['Stacking'][2] += ' '+stack
2109	return Layer
2110
2111	def postURL(URL,postdict):
2112	'''Posts a set of values as from a web form. If access fails to an https
2113	site the access is retried with http.
2114
2115	:param str URL: the URL to post; typically something
2116	like 'http://www.../dir/page?'
2117	:param dict postdict: contains keywords and values, such
2118	as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2119	:returns: a string with the response from the web server or None
2120	if access fails.
2121	'''
2122	try:
2123	import requests # delay this until now, since rarely needed
2124	except:
2125	# this import seems to fail with the Anaconda pythonw on
2126	# macs; it should not!
2127	print('Warning: failed to import requests. Python config error')
2128	return None
2129
2130	repeat = True
2131	while repeat:
2132	r = None
2133	repeat = False
2134	try:
2135	r = requests.get(URL,params=postdict)
2136	if r.status_code == 200:
2137	print('request OK')
2138	page = r.text
2139	return page # success
2140	else:
2141	print('request to {} failed. Reason={}'.format(URL,r.reason))
2142	except Exception as msg: #ConnectionError?
2143	print('connection error - not on internet?')
2144	if GSASIIpath.GetConfigValue('debug'): print(msg)
2145	finally:
2146	if r: r.close()
2147	if URL.startswith('https:'):
2148	repeat = True
2149	URL = URL.replace('https:','http:')
2150	else:
2151	return None
2152
2153	if __name__ == '__main__':
2154	import GSASIIdataGUI
2155	application = GSASIIdataGUI.GSASIImain(0)
2156	G2frame = application.main
2157	#app = wx.PySimpleApp()
2158	#G2frame = wx.Frame(None) # create a frame
2159	#frm.Show(True)
2160	#filename = '/tmp/notzip.zip'
2161	#filename = '/tmp/all.zip'
2162	#filename = '/tmp/11bmb_7652.zip'
2163
2164	#selection=None, confirmoverwrite=True, parent=None
2165	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2166	#print ExtractFileFromZip(filename,multipleselect=True)
2167	# #confirmread=False, confirmoverwrite=False)
2168
2169	# choicelist=[ ('a','b','c'),
2170	# ('test1','test2'),('no choice',)]
2171	# titles = [ 'a, b or c', 'tests', 'No option here']
2172	# dlg = MultipleChoicesDialog(
2173	# choicelist,titles,
2174	# parent=frm)
2175	# if dlg.ShowModal() == wx.ID_OK:
2176	# print 'Got OK'
2177	imagefile = '/tmp/NDC5_00237_3.ge3'
2178	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2179
2180	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2181
2182	GSASIIpath.IPyBreak_base()

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